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Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments.

Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS - Nucleic Acids Res. (2007)

Bottom Line: We have developed a centralized database with an easy-to-use interface, Cyclebase.org, for viewing and downloading these data.The user interface facilitates searches for genes of interest as well as downloads of genome-wide results.Furthermore, state-of-the-art computational analyses provide key information on both individual experiments and combined datasets such as whether or not a gene is periodically expressed and, if so, the time of peak expression.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark.

ABSTRACT
The past decade has seen the publication of a large number of cell-cycle microarray studies and many more are in the pipeline. However, data from these experiments are not easy to access, combine and evaluate. We have developed a centralized database with an easy-to-use interface, Cyclebase.org, for viewing and downloading these data. The user interface facilitates searches for genes of interest as well as downloads of genome-wide results. Individual genes are displayed with graphs of expression profiles throughout the cell cycle from all available experiments. These expression profiles are normalized to a common timescale to enable inspection of the combined experimental evidence. Furthermore, state-of-the-art computational analyses provide key information on both individual experiments and combined datasets such as whether or not a gene is periodically expressed and, if so, the time of peak expression. Cyclebase is available at http://www.cyclebase.org.

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Benchmark of methods for identifying cell-cycle regulated genes. For each of the four organisms, a benchmark set was compiled of genes whose promoters are bound by known cell-cycle transcription factors (16,29,30), under the assumption that these genes should be highly overlapping with those that display cell-cycle regulation at the transcriptional level (i.e. periodic expression). The panels show the fraction of a benchmark set retrieved as a function of the number of genes suggested for each individual method (1,2,5–28). Better methods should therefore be towards the upper left corner of the plot. Methods which provide a ranked list of genes are displayed as a line, whereas those that only supply an unranked set of genes appear in the plots as cross mark/plus sign. The black dotted line corresponds to picking genes randomly. In all four organisms, the combined analysis of all data within an organism presented by Cyclebase outperforms all existing methods or suggested sets of periodically expressed genes. In all organisms, the curves eventually display the same slope as the random performance curve (black dotted), indicating that including more genes from this point on yields no enrichment in genes from the benchmark set.
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Figure 2: Benchmark of methods for identifying cell-cycle regulated genes. For each of the four organisms, a benchmark set was compiled of genes whose promoters are bound by known cell-cycle transcription factors (16,29,30), under the assumption that these genes should be highly overlapping with those that display cell-cycle regulation at the transcriptional level (i.e. periodic expression). The panels show the fraction of a benchmark set retrieved as a function of the number of genes suggested for each individual method (1,2,5–28). Better methods should therefore be towards the upper left corner of the plot. Methods which provide a ranked list of genes are displayed as a line, whereas those that only supply an unranked set of genes appear in the plots as cross mark/plus sign. The black dotted line corresponds to picking genes randomly. In all four organisms, the combined analysis of all data within an organism presented by Cyclebase outperforms all existing methods or suggested sets of periodically expressed genes. In all organisms, the curves eventually display the same slope as the random performance curve (black dotted), indicating that including more genes from this point on yields no enrichment in genes from the benchmark set.

Mentions: Based on independent benchmarking, this methodology has previously been proven to be as good as or superior to all other published methods for identifying periodically expressed genes (16,29,30). We have expanded this benchmark to also include recent methods (1,2,5–28) and experiments (Figure 2). Benchmark sets were compiled that are enriched in cell-cycle regulated genes from targets of known cell-cycle transcription factors (16,29,30). We benchmarked each method's; ability to retrieve genes in these sets. Figure 2 displays the benchmarking results, which shows that the method used in Cyclebase provides clear improvements over other methods and that combining all data for an organism is, not surprisingly, superior to any single dataset analyzed on its own. Based on the benchmarks, we have selected a set of significantly periodically expressed genes within each organism (labeled with a small ‘Periodic’ icon). We found 600 periodic genes in budding yeast, 500 in fission yeast, 600 in human and 400 in the plant A. thaliana. For these periodic genes, we compute the ‘peaktime’ based on all available expression profiles (16).Figure 2.


Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments.

Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS - Nucleic Acids Res. (2007)

Benchmark of methods for identifying cell-cycle regulated genes. For each of the four organisms, a benchmark set was compiled of genes whose promoters are bound by known cell-cycle transcription factors (16,29,30), under the assumption that these genes should be highly overlapping with those that display cell-cycle regulation at the transcriptional level (i.e. periodic expression). The panels show the fraction of a benchmark set retrieved as a function of the number of genes suggested for each individual method (1,2,5–28). Better methods should therefore be towards the upper left corner of the plot. Methods which provide a ranked list of genes are displayed as a line, whereas those that only supply an unranked set of genes appear in the plots as cross mark/plus sign. The black dotted line corresponds to picking genes randomly. In all four organisms, the combined analysis of all data within an organism presented by Cyclebase outperforms all existing methods or suggested sets of periodically expressed genes. In all organisms, the curves eventually display the same slope as the random performance curve (black dotted), indicating that including more genes from this point on yields no enrichment in genes from the benchmark set.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238932&req=5

Figure 2: Benchmark of methods for identifying cell-cycle regulated genes. For each of the four organisms, a benchmark set was compiled of genes whose promoters are bound by known cell-cycle transcription factors (16,29,30), under the assumption that these genes should be highly overlapping with those that display cell-cycle regulation at the transcriptional level (i.e. periodic expression). The panels show the fraction of a benchmark set retrieved as a function of the number of genes suggested for each individual method (1,2,5–28). Better methods should therefore be towards the upper left corner of the plot. Methods which provide a ranked list of genes are displayed as a line, whereas those that only supply an unranked set of genes appear in the plots as cross mark/plus sign. The black dotted line corresponds to picking genes randomly. In all four organisms, the combined analysis of all data within an organism presented by Cyclebase outperforms all existing methods or suggested sets of periodically expressed genes. In all organisms, the curves eventually display the same slope as the random performance curve (black dotted), indicating that including more genes from this point on yields no enrichment in genes from the benchmark set.
Mentions: Based on independent benchmarking, this methodology has previously been proven to be as good as or superior to all other published methods for identifying periodically expressed genes (16,29,30). We have expanded this benchmark to also include recent methods (1,2,5–28) and experiments (Figure 2). Benchmark sets were compiled that are enriched in cell-cycle regulated genes from targets of known cell-cycle transcription factors (16,29,30). We benchmarked each method's; ability to retrieve genes in these sets. Figure 2 displays the benchmarking results, which shows that the method used in Cyclebase provides clear improvements over other methods and that combining all data for an organism is, not surprisingly, superior to any single dataset analyzed on its own. Based on the benchmarks, we have selected a set of significantly periodically expressed genes within each organism (labeled with a small ‘Periodic’ icon). We found 600 periodic genes in budding yeast, 500 in fission yeast, 600 in human and 400 in the plant A. thaliana. For these periodic genes, we compute the ‘peaktime’ based on all available expression profiles (16).Figure 2.

Bottom Line: We have developed a centralized database with an easy-to-use interface, Cyclebase.org, for viewing and downloading these data.The user interface facilitates searches for genes of interest as well as downloads of genome-wide results.Furthermore, state-of-the-art computational analyses provide key information on both individual experiments and combined datasets such as whether or not a gene is periodically expressed and, if so, the time of peak expression.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark.

ABSTRACT
The past decade has seen the publication of a large number of cell-cycle microarray studies and many more are in the pipeline. However, data from these experiments are not easy to access, combine and evaluate. We have developed a centralized database with an easy-to-use interface, Cyclebase.org, for viewing and downloading these data. The user interface facilitates searches for genes of interest as well as downloads of genome-wide results. Individual genes are displayed with graphs of expression profiles throughout the cell cycle from all available experiments. These expression profiles are normalized to a common timescale to enable inspection of the combined experimental evidence. Furthermore, state-of-the-art computational analyses provide key information on both individual experiments and combined datasets such as whether or not a gene is periodically expressed and, if so, the time of peak expression. Cyclebase is available at http://www.cyclebase.org.

Show MeSH